VMD-L Mailing List

From: ehsan zahedinejad (ehsanzahedinejad_at_gmail.com)
Date: Thu Sep 13 2012 - 18:53:39 CDT

Dear VMD users,

After successfully generating ff parameters using VMD fftk I have a
question about duplicate option in fftk. I used this option to get the best
dihedral fit. After extracting ff from dihedral I noticed there are two set
of dihedrals for one of my dihedral parameter (B/C I duplicated this set
during the process of opt- torsions). For example I have the following
duplicated form in my ff output files:

C6 C7 C8 O5 0.6670 1 0.00
C6 C7 C8 O5 0.7860 3 0.00

My question is which one of these dihedral will be used by MD engine. Or
should I remove one of them from my final ff file? If so which one has to
be removed?

any suggestions are welcome.

Ehsan.